ALCOdb: Gene Coexpression Database for Microalgae.
ALCOdb: Gene Coexpression Database for Microalgae.
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DOI：
10.1093/pcp/pcv190
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发表时间：
2016-01
影响因子：
4.9
通讯作者：
Obayashi T
中科院分区：
文献类型：
--
作者：
Aoki Y;Okamura Y;Ohta H;Kinoshita K;Obayashi T
在能源和粮食短缺的时代，微藻作为有前途的生物燃料和食品原料来源受到了广泛关注。然而，只有一小部分的微藻基因的功能特征。在这里，我们已经开发了藻类基因共表达数据库（ALCOdb; http://alcodb.jp），它提供了基因共表达信息，以调查基因模块的功能。ALCOdb目前支持两种模式藻类：绿色衣藻和红色衣藻。用户可以通过三个独特的数据页面检索感兴趣基因的共表达信息：（i）共表达基因列表;（ii）基因信息;和（iii）共表达基因网络。除了基本的共表达信息，ALCOdb还提供了几个高级功能，如表达谱查看器和差异表达基因搜索工具。使用这些用户界面，我们证明了我们的基因共表达数据有可能检测功能相关的基因，并有助于推断未表征基因的生物学作用。ALCOdb将促进微藻生物现象的分子和生物化学研究，如脂质代谢和细胞器发育，并促进植物细胞系统的进化理解。
In the era of energy and food shortage, microalgae have gained much attention as promising sources of biofuels and food ingredients. However, only a small fraction of microalgal genes have been functionally characterized. Here, we have developed the Algae Gene Coexpression database (ALCOdb; http://alcodb.jp), which provides gene coexpression information to survey gene modules for a function of interest. ALCOdb currently supports two model algae: the green alga Chlamydomonas reinhardtii and the red alga Cyanidioschyzon merolae. Users can retrieve coexpression information for genes of interest through three unique data pages: (i) Coexpressed Gene List; (ii) Gene Information; and (iii) Coexpressed Gene Network. In addition to the basal coexpression information, ALCOdb also provides several advanced functionalities such as an expression profile viewer and a differentially expressed gene search tool. Using these user interfaces, we demonstrated that our gene coexpression data have the potential to detect functionally related genes and are useful in extrapolating the biological roles of uncharacterized genes. ALCOdb will facilitate molecular and biochemical studies of microalgal biological phenomena, such as lipid metabolism and organelle development, and promote the evolutionary understanding of plant cellular systems.